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Table 2 Pearson's Product Moment Correlation Coefficients among barley gene expression indices calculated from seven different methods.

From: Methods for evaluating gene expression from Affymetrix microarray datasets

Method

AD

MAS5.0

MBEI1

MBEI2

RMA

GCRMA

PDNN

AD

0.991 ± 0.005

0.975 ± 0.004

0.988 ± 0.001

0.985 ± 0.001

0.647 ± 0.007

0.791 ± 0.008

0.615 ± 0.007

MAS5.0

0.973

0.984 ± 0.009

0.961 ± 0.005

0.965 ± 0.003

0.619 ± 0.026

0.748 ± 0.024

0.583 ± 0.026

MBEI1

0.987

0.958

0.990 ± 0.005

0.988 ± 0.001

0.664 ± 0.011

0.797 ± 0.009

0.629 ± 0.008

MBEI2

0.985

0.963

0.988

0.990 ± 0.005

0.643 ± 0.006

0.774 ± 0.006

0.605 ± 0.006

RMA

0.647

0.616

0.662

0.643

0.993 ± 0.003

0.914 ± 0.002

0.939 ± 0.008

GCRMA

0.791

0.744

0.797

0.774

0.914

0.992 ± 0.005

0.923 ± 0.004

PDNN

0.614

0.581

0.628

0.604

0.940

0.923

0.992 ± 0.005

  1. The upper triangle shows the mean and corresponding standard deviation of 24 correlation coefficients, r ijk , (k = 1, 2,..., 24). r ijk represents the correlation coefficient between 22,840 corresponding pairs of gene expression indices calculated by methods i and j from the kth microarray sample. The diagonal cells show means and standard deviations of 24 correlation coefficients, r imn (n = 1, 2, 3 and m = 1, 2,..., 8). For n = 1, 2, 3, r imn corresponds to three correlation coefficients calculated from three possible pairs of replicates for the mth cultivar (m = 1, 2,..., 8) using method i. The lower triangle shows the correlation coefficients between all pairs of 22,840 gene expression indices calculated from methods i and j across all k = 24 samples.
  2. 1 MBEI PM only model
  3. 2 MBEI PM-MM model